mirror of
https://github.com/MillironX/nf-core_modules.git
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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
98 lines
5.2 KiB
YAML
98 lines
5.2 KiB
YAML
- name: pirate test_pirate
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command: nextflow run ./tests/modules/pirate -entry test_pirate -c ./tests/config/nextflow.config -c ./tests/modules/pirate/nextflow.config
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tags:
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- pirate
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files:
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- path: output/pirate/results/PIRATE.gene_families.ordered.tsv
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contains: ["allele_name"]
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- path: output/pirate/results/PIRATE.gene_families.tsv
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contains: ["allele_name"]
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- path: output/pirate/results/PIRATE.genomes_per_allele.tsv
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contains: ["g0197"]
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- path: output/pirate/results/PIRATE.log
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contains: ["PIRATE input options"]
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- path: output/pirate/results/PIRATE.pangenome_summary.txt
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md5sum: 4551c291bc06b21f984f25c09329ed7d
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- path: output/pirate/results/PIRATE.unique_alleles.tsv
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contains: ["allele_name"]
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- path: output/pirate/results/binary_presence_absence.fasta
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contains: ["GCF_000292685"]
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- path: output/pirate/results/binary_presence_absence.nwk
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md5sum: 5b5d86bf97d97de37bb9db514abb7762
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- path: output/pirate/results/cluster_alleles.tab
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contains: ["g0001"]
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- path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
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md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
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- path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
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md5sum: a24d6048b3074242bb558c7fa27a8b03
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- path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
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md5sum: 0c08228585f4fa95686e9b025e0fe9c1
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- path: output/pirate/results/genome2loci.tab
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md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
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- path: output/pirate/results/genome_list.txt
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md5sum: 6534b1635c258ad92b829077addc1ff5
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- path: output/pirate/results/link_clusters.log
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contains: ["parsing paralog file"]
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- path: output/pirate/results/loci_list.tab
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/loci_paralog_categories.tab
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md5sum: 6404d2a32526a398f42d7da768a389bd
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- path: output/pirate/results/modified_gffs/GCF_000292685.gff
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md5sum: 2b73bda2f84dc634303dc90e641040ca
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- path: output/pirate/results/modified_gffs/GCF_000298385.gff
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md5sum: b1a9d6557d47e09249f08a7acdbbd618
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- path: output/pirate/results/modified_gffs/GCF_002849995.gff
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md5sum: 68532fc9bb639e6d83c731a069f60cf8
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- path: output/pirate/results/pan_sequences.fasta
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md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
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- path: output/pirate/results/pangenome.connected_blocks.tsv
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contains: ["block_number"]
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- path: output/pirate/results/pangenome.edges
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contains: ["g0259"]
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- path: output/pirate/results/pangenome.gfa
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contains: ["g0001"]
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- path: output/pirate/results/pangenome.order.tsv
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contains: ["g0172"]
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- path: output/pirate/results/pangenome.reversed.tsv
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md5sum: b2396ce09a6e4178761eca6dc7f4434f
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- path: output/pirate/results/pangenome.syntenic_blocks.tsv
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contains: ["g0091"]
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- path: output/pirate/results/pangenome.temp
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- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
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md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
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- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
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contains: ["GCF_000298385_00081"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
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contains: ["GCF_000298385_00242"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
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contains: ["chaos"]
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
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md5sum: 84668b6c65b57026a17a50b0edd02541
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
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- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto
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- path: output/pirate/results/pangenome_log.txt
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contains: ["Creating pangenome on amino acid"]
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- path: output/pirate/results/paralog_clusters.tab
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contains: ["g0216"]
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- path: output/pirate/results/representative_sequences.faa
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contains: ["representative_genome"]
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- path: output/pirate/results/representative_sequences.ffn
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contains: ["representative_genome"]
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- path: output/pirate/results/split_groups.log
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contains: ["g0213"]
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